jPAP Manual > V. Defining a Genetic Model

The ModEd window is used to define the model to be used when running a jPAP analysis command from the Project Window. jPAP can assume a variety of genetic models related to any number of markers and traits. Different parameterizations are available to define the model.

An overview of the ModEd interface was provided earlier, as part of the jPAP interface tour. This chapter digs into the meaning of the various global options available for selection in defining a model, and how they fit into the larger package. The intent is to present the information necessary to define an appropriate parameterization. The first section will survey the Genotype Assignment (GA) Node settings, while subsequent sections walk through the parameterizations provided by the installed Pedigree Analysis Module (PAM) implementations, available on the PAMSelections Node.

Throughout this chapter and elsewhere in the manual, a convenient shorthand will be adopted to refer to specific options on the latter node. In the property pane for the node, you'll note that each roster of PAMs has a short ID string in brackets, and so does each PAM in a given roster's drop-down selection list. By concatenating these two strings one obtains a global ID that can be used to refer to a specific PAM. This convention should also prove helpful to PAP users making the transition to jPAP, since these global IDs are identical to the names of the corresponding PAP subroutines.

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